Just to throw more ideas out:
The cinematics suggest the mind flayers are dying. There were already many mind flayers who were dying before the attack and crash. Perhaps the tadpoles is their last ditch effort to survive as a species?
I think it's a little less of a leap to assume he is weak because they are being hunted and attacked by Gith, not because of some species wide cancer of anything.
Yes! Even the first time I watched the opening I felt really bad for that lonesome mind flayer. Poor guy (really!). All his friends are dead, he has to take care of a whole ship on his own, the nursery, the elder-y brains in jars, escaping githianky and then fighting off all the devils and cambions who try to kill him on sight. Then he tries to VERY GENTLY mind control a bunch of fishermen to survive and gets offed for his efforts. Then he gets taken to a stinky goblin camp, his cadaver interrogated by people who clearly can't properly interpret mind-speech, and probably burned. If anyone deserved an afterlife upgrade, it's him.
He was not alone on the ship -- you pass by several Illithid corpses which appears to have been killed by imps, and there's a second Illithid at the helm who appears in the cut scene where he is killed by the imps as you enter the room.
